Owens Valley. Mt. Whitney Packers and Owens Valley History site. Hosted by Bruce Morgan. Lots of interesting historical segments, with some photos.  [ccr]
http://www.owensvalleyhistory.com/ 

Ghost towns of the West.  This site has cascading clickable maps and some fantastic photos.  Included are over one hundred towns in eight states:  Arizona, California, Colorado, Idaho, Montana, Nevada, New Mexico, and Utah.  [ccr]
http://www.ghosttowngallery.com/htme/map.htm

The California Environment.  A great variety of environmentally-related California images, from all over the state; mostly photos.  From the UC Berkeley Geo-Images Project.  [ccr]                        
http://geoimages.berkeley.edu/GeoImages/BainCalif/CalClickMap.html

Alternative Futures, Camp Pendleton.  Focusing on biodiversity and landscape planning, this site has numerous maps and analyses.   From a study funded in part by the U. S. Environmental Protection Agency.  [ccr]
http://www.gsd.harvard.edu/studios/brc/brc.html

Polyland.  This comprehensive site focuses on 10,000 acres surrounding California Polytechnic State University, San Luis Obispo.  The site incorporates contributions from students and faculty at the university who have used the area as a laboratory for the study of environmental aspects, sustainability, and other characteristics of this place.  Sections include agriculture, climate, geology, flora, history, recreation, soils, and other topics, and the site makes generous use of maps and photos. (Suggested by Steven Marx.)  [ccr]
http://polyland.calpoly.edu/overview/index.html

Japantown Atlas.   Maps of Japanese-American communities in two dozen California cities, just prior to World War II and internment.   Detailed maps showing businesses, instutions, and other features are based on 1940 Sanborn maps.  The Japantown Atlas Project is directed by Ben Peace and funded by the California State Library. 
http://japantownatlas.com/

California Japantowns.  This site includes map-based virtual tours of traditional Japanese neighborhoods in San Francisco, San Jose, and Los Angeles.  [ccr]
http://www.californiajapantowns.org/index.html 

California Coastline.   Close-up photos of virtually all of the coast, selectable from maps.  This site is so detailed and comprehensive that some have protested it as an invasion of privacy.  [ccr]
http://www.californiacoastline.org/

Geologic Tours of Southern California.  A series of virtual field trips to interesting geological settings, illustrated with maps and photos. Locations range from Red Rock Canyon on the north to the Salton Trough on the south.  Created by geologists at California State University, Long Beach. [ccr]
http://seis.natsci.csulb.edu/VIRTUAL_FIELD/vfmain.htm 

Historic California. Some fantastic historical images of various parts of the state from lantern slides. From the UC Berkeley Geo-Images Project.  [ccr] http://geoimages.berkeley.edu/GeoImages/LanternSlides/LanternSlides_TOC.html

California highways.  Interesting historic photos and maps from various parts of the state, for the highway lover.  [ccr]
http://members.cox.net/mkpl2/hist/hist.html

Digital Atlases, Searchable Digital Archives, and Other Sites Useful for Exploring Places

OakMapper webGIS Application.  The OakMapper webGIS application allows users to learn about Sudden Oak Death distribution in California. The site is maintained by the University of California's Center for the Assessment and Monitoring of Forest and Environmental Resources (CAMFER).  [tdh]
http://www.oakmapper.org

California Atlas of Panoramic Aerial Images.   A map-base collection of medium-scale images across the state, including many that are rather spectacular.  Created by William A. Bowen through the auspices of the California Geographical Survey at CSU Northridge.  [ccr]  
http://130.166.124.2/ca_panorama_atlas/index.html

Digital Atlas of California.  Great maps of various population characterstics, including race, income, citizenship, education, and poverty, mostly from the 1990 U. S. Census.   Links also to similar atlases for San Francisco, Los Angeles, San Diego, and Sacramento.   Another contribution of William Bowen and the California Geographical Society.  [ccr]
http://130.166.124.2/CApage1.html